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pep8/pyflakes
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@ -36,17 +36,23 @@
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from __future__ import print_function
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from PIL import Image, ImageFile
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import os, struct, sys
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import os
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import struct
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import sys
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def isInt(f):
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try:
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i = int(f)
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if f-i == 0: return 1
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else: return 0
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if f-i == 0:
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return 1
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else:
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return 0
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except:
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return 0
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iforms = [1,3,-11,-12,-21,-22]
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iforms = [1, 3, -11, -12, -21, -22]
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# There is no magic number to identify Spider files, so just check a
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# series of header locations to see if they have reasonable values.
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@ -56,28 +62,32 @@ iforms = [1,3,-11,-12,-21,-22]
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def isSpiderHeader(t):
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h = (99,) + t # add 1 value so can use spider header index start=1
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# header values 1,2,5,12,13,22,23 should be integers
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for i in [1,2,5,12,13,22,23]:
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if not isInt(h[i]): return 0
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for i in [1, 2, 5, 12, 13, 22, 23]:
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if not isInt(h[i]):
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return 0
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# check iform
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iform = int(h[5])
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if not iform in iforms: return 0
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if iform not in iforms:
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return 0
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# check other header values
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labrec = int(h[13]) # no. records in file header
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labbyt = int(h[22]) # total no. of bytes in header
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lenbyt = int(h[23]) # record length in bytes
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#print "labrec = %d, labbyt = %d, lenbyt = %d" % (labrec,labbyt,lenbyt)
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if labbyt != (labrec * lenbyt): return 0
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# print "labrec = %d, labbyt = %d, lenbyt = %d" % (labrec,labbyt,lenbyt)
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if labbyt != (labrec * lenbyt):
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return 0
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# looks like a valid header
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return labbyt
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def isSpiderImage(filename):
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fp = open(filename,'rb')
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fp = open(filename, 'rb')
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f = fp.read(92) # read 23 * 4 bytes
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fp.close()
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t = struct.unpack('>23f',f) # try big-endian first
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t = struct.unpack('>23f', f) # try big-endian first
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hdrlen = isSpiderHeader(t)
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if hdrlen == 0:
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t = struct.unpack('<23f',f) # little-endian
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t = struct.unpack('<23f', f) # little-endian
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hdrlen = isSpiderHeader(t)
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return hdrlen
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@ -94,11 +104,11 @@ class SpiderImageFile(ImageFile.ImageFile):
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try:
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self.bigendian = 1
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t = struct.unpack('>27f',f) # try big-endian first
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t = struct.unpack('>27f', f) # try big-endian first
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hdrlen = isSpiderHeader(t)
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if hdrlen == 0:
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self.bigendian = 0
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t = struct.unpack('<27f',f) # little-endian
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t = struct.unpack('<27f', f) # little-endian
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hdrlen = isSpiderHeader(t)
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if hdrlen == 0:
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raise SyntaxError("not a valid Spider file")
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@ -110,7 +120,7 @@ class SpiderImageFile(ImageFile.ImageFile):
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if iform != 1:
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raise SyntaxError("not a Spider 2D image")
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self.size = int(h[12]), int(h[2]) # size in pixels (width, height)
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self.size = int(h[12]), int(h[2]) # size in pixels (width, height)
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self.istack = int(h[24])
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self.imgnumber = int(h[27])
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@ -139,9 +149,10 @@ class SpiderImageFile(ImageFile.ImageFile):
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self.rawmode = "F;32F"
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self.mode = "F"
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self.tile = [("raw", (0, 0) + self.size, offset,
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(self.rawmode, 0, 1))]
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self.__fp = self.fp # FIXME: hack
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self.tile = [
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("raw", (0, 0) + self.size, offset,
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(self.rawmode, 0, 1))]
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self.__fp = self.fp # FIXME: hack
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# 1st image index is zero (although SPIDER imgnumber starts at 1)
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def tell(self):
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@ -174,6 +185,7 @@ class SpiderImageFile(ImageFile.ImageFile):
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from PIL import ImageTk
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return ImageTk.PhotoImage(self.convert2byte(), palette=256)
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# --------------------------------------------------------------------
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# Image series
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@ -198,14 +210,16 @@ def loadImageSeries(filelist=None):
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imglist.append(im)
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return imglist
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# --------------------------------------------------------------------
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# For saving images in Spider format
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def makeSpiderHeader(im):
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nsam,nrow = im.size
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nsam, nrow = im.size
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lenbyt = nsam * 4 # There are labrec records in the header
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labrec = 1024 / lenbyt
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if 1024%lenbyt != 0: labrec += 1
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if 1024 % lenbyt != 0:
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labrec += 1
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labbyt = labrec * lenbyt
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hdr = []
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nvalues = int(labbyt / 4)
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@ -216,13 +230,13 @@ def makeSpiderHeader(im):
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return []
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# NB these are Fortran indices
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hdr[1] = 1.0 # nslice (=1 for an image)
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hdr[2] = float(nrow) # number of rows per slice
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hdr[5] = 1.0 # iform for 2D image
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hdr[12] = float(nsam) # number of pixels per line
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hdr[13] = float(labrec) # number of records in file header
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hdr[22] = float(labbyt) # total number of bytes in header
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hdr[23] = float(lenbyt) # record length in bytes
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hdr[1] = 1.0 # nslice (=1 for an image)
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hdr[2] = float(nrow) # number of rows per slice
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hdr[5] = 1.0 # iform for 2D image
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hdr[12] = float(nsam) # number of pixels per line
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hdr[13] = float(labrec) # number of records in file header
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hdr[22] = float(labbyt) # total number of bytes in header
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hdr[23] = float(lenbyt) # record length in bytes
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# adjust for Fortran indexing
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hdr = hdr[1:]
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@ -230,9 +244,10 @@ def makeSpiderHeader(im):
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# pack binary data into a string
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hdrstr = []
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for v in hdr:
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hdrstr.append(struct.pack('f',v))
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hdrstr.append(struct.pack('f', v))
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return hdrstr
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def _save(im, fp, filename):
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if im.mode[0] != "F":
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im = im.convert('F')
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@ -248,11 +263,12 @@ def _save(im, fp, filename):
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raise IOError("Unable to open %s for writing" % filename)
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fp.writelines(hdr)
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rawmode = "F;32NF" #32-bit native floating point
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ImageFile._save(im, fp, [("raw", (0,0)+im.size, 0, (rawmode,0,1))])
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rawmode = "F;32NF" # 32-bit native floating point
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ImageFile._save(im, fp, [("raw", (0, 0)+im.size, 0, (rawmode, 0, 1))])
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fp.close()
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def _save_spider(im, fp, filename):
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# get the filename extension and register it with Image
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fn, ext = os.path.splitext(filename)
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@ -290,5 +306,7 @@ if __name__ == "__main__":
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if outfile != "":
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# perform some image operation
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im = im.transpose(Image.FLIP_LEFT_RIGHT)
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print("saving a flipped version of %s as %s " % (os.path.basename(filename), outfile))
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print(
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"saving a flipped version of %s as %s " %
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(os.path.basename(filename), outfile))
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im.save(outfile, "SPIDER")
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